In Okular (for desktop), you can set keyboard shortcuts for various color inversion/shifting modes. Or you can permanently set one in the Accessibility settings.
Yeah I wasn't sure, but the first pdf reader I thought of was librera. Pretty sure Okular can do it too. Normally the "dark mode" is just inverting the colours since printed pdfs are normally black text on white paper.
Not FOSS but free - ReadEra, it's working extremely well. No ads or anything, the only feature the paid version has is cloud sync of your library, and sync reading progress across devices.
Been using it for 8 years or so, bought it at some point just because it works without a hitch since basically forever.